Great War

He was appointed in command of the destroyer Walker on 5 January, 1918.[10]

Post-War

On 9 January, 1920, Mackinnon was appointed in command of the flotilla leader Shakespeare.[11]

On 17 March, 1921, Mackinnon was subjected to a Court Martial for testing the engines of Shakespeare in a tidal basin while men were painting her sides from a catamaran. A charge that he had endangered their lives was not proved and he was acquitted.[12]

Mackinnon was appointed to Montrose, additional, on 15 September, 1924 and then in command upon her commissioning on 1 October, becoming then Captain (D) of the Fourth Destroyer Flotilla. He retained command of 4 D.F. when he was appointed in command of Broke on 10 February, 1925.[14]

In February, 1932, Mackinnon issued an adverse report on his executive officer, Commander F. R. Baxter in Hermes in which he criticised Baxter's social grace and excessive self-regard. Mackinnon was informed that Their Lordships did not concur. Mackinnon was invalided from the China Station that year with diphtheria. He was admitted to Chatham hospital in July.[15]